I'd have Superman primarily battle with Metallo & Intergang. Lex Luthor is prominent in the film as a behind-the-scenes baddie but, to the public, his hands are clean. Maybe even end the film with Lex being the one who stops Metallo (maybe he installed a failsafe?).

And, of course, end the film with a verbal showdown between the two as Superman flies into Luthor's office (classic scenario between the two that could have a lot of emotional punch as the film closes).

MOS3:

Brainiac comes to town, wants to harness all the technology & information of Earth; just as he did throughout the cosmos. (He was going to destroy Krypton, but saw that it was doomed anyway and allowed fate to take its course).

Idk how the plot would work out, but at the end, we get Lexiac (Lex & Brainiac fused together), and that way, we can get a satisfying physical confrontation for the ages: Lex Luthor vs. Superman.

This will be a rivalry that has spanned two films, so it would hold some real weight and be a great way to cap out a trilogy (not that they need to end at 3, but it'd be a nice end to Luthor's saga).